Build issue

.github/workflows/build.yml

@@ -0,0 +1,27 @@
+# Builds the repository using mamba
+
+---
+name: build
+
+on: 
+  push:
+  pull_request:
+  schedule:
+      - cron: '0 0 * * 0'
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [macos-12, macos-14, ubuntu-latest, windows-latest]
+        envs: [binder/environment.yml]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+      - name: Install Conda environment for ${{ matrix.envs }} with Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ${{ matrix.envs }}

.gitignore

@@ -2,3 +2,4 @@ venv
 .DS_Store
 *.pyc
 _*
+*.ipynb_checkpoints

.readthedocs.yaml

@@ -17,7 +17,7 @@ sphinx:
 formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
-python:
-  version: 3.7
-  install:
-    - requirements: requirements.txt
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"

README.md

@@ -1,29 +1,62 @@
 # Guide on how to integrate ilastik and OMERO
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ome/omero-guide-ilastik/master?filepath=notebooks)
 [![Documentation Status](https://readthedocs.org/projects/omero-guide-ilastik/badge/?version=latest)](https://omero-guides.readthedocs.io/en/latest/ilastik/docs/index.html)
-[![Actions Status](https://github.com/ome/omero-guide-ilastik/workflows/repo2docker/badge.svg)](https://github.com/ome/omero-guide-ilastik/actions)
+[![Actions Status](https://github.com/ome/omero-guide-ilastik/workflows/build/badge.svg)](https://github.com/ome/omero-guide-ilastik/actions)
 
 The documentation is deployed at [Use Ilastik](https://omero-guides.readthedocs.io/en/latest/ilastik/docs/index.html).
 
 This guide demonstrates how to use ilastik to analyze data stored in [IDR](https://idr.openmicroscopy.org/) or an OMERO server.
 
 This repository contains documentation and notebooks.
 
-To run the notebooks, you can either [run on mybinder.org](https://mybinder.org/v2/gh/ome/omero-guide-ilastik/master?filepath=notebooks) or build locally with [repo2docker](https://repo2docker.readthedocs.io/).
+Running locally:
 
-To build locally:
+Finally, if you would like to install the necessary requirements locally,
+we suggest using Mamba:
 
- * Install [Docker](https://www.docker.com/) if required
- * Open a terminal as administrator
- * Create a virtual environment and install repo2docker from PyPI.
- * Clone this repository
- * Run ``repo2docker``
+* If you do not have any pre-existing conda installation, [install Mamba](https://mamba.readthedocs.io/en/latest/installation.html#installation) and use [mambaforge](https://github.com/conda-forge/miniforge#mambaforge). 
+* In case you have a pre-existing conda installation, you can install Mamba by either:
+  - Using the recommended way to install Mamba from [mambaforge](https://github.com/conda-forge/miniforge#mambaforge). This will not invalidate your conda installation, but possibly your pre-existing conda envs will be in a different location (e.g. ``/Users/USER_NAME/opt/anaconda3/envs/``) then the new mamba envs (e.g. ``/Users/USER_NAME/mambaforge/envs/``). You can verify this by running ``conda env list``. The addition of ``export CONDA_ENVS_PATH=/Users/user/opt/anaconda3/envs/`` into your ``.bashprofile`` or ``.zprofile`` file will fix this. 
+  - Use the [Existing conda install](https://mamba.readthedocs.io/en/latest/installation.html#existing-conda-install) way, i.e. run ``conda install mamba -n base -c conda-forge`` whilst in the base environment. This way can take much longer time than the recommended way described above, and might not lead to a successful installation, especially if run on arm64 (Apple Silicon) OS X.
 
-```
-pip install jupyter-repo2docker
-git clone https://github.com/ome/omero-guide-ilastik.git
-cd omero-guide-ilastik
-repo2docker .
+Create the environment running the commands below as written:
+
+For Windows, OS X x86_64 (NOT arm64 Apple Silicon), Linux:
+
+    $ git clone https://github.com/ome/omero-guide-ilastik
+
+    $ cd omero-guide-ilastik
+
+    $ mamba env create -f binder/environment.yml
+
+For OS X arm64 Apple Silicon
+
+    $ git clone https://github.com/ome/omero-guide-ilastik 
+
+    $ cd omero-guide-ilastik
+
+    $ CONDA_SUBDIR=osx-64 mamba env create -f binder/environment.yml
+
+and activate the newly created environment:
+
+    $ conda activate omero-guide-ilastik
+
+
+Before creating a new environment, remember to deactivate the current one:
+
+    $ conda deactivate
+
+See also [Conda command reference](https://docs.conda.io/projects/conda/en/latest/commands.html).
+
+The following steps are only required if you want to run the notebooks.
+
+* If you have Anaconda installed:
+  * Start Jupyter from the Anaconda-navigator
+  * To register the environment, run ``python -m ipykernel install --user --name omero-guide-ilastik``
+  * Select the notebook you wish to run and select the ``Kernel>Change kernel>Python [conda env:omero-guide-ilastik]`` or ``Kernel>Change kernel>omero-guide-ilastik``
+* If Anaconda is not installed:
+  * Open jupyter notebook i.e. ``jupyter notebook`` and select the ``omero-guide-ilastik`` kernel or ``[conda env:omero-guide-ilastik]`` according to what is available.
+
+  To stop the notebook server, in the terminal where te server is running, press ``Ctrl C``. The following question will be asked in the terminal ``Shutdown this notebook server (y/[n])?``. Enter the desired choice.
 ```
 
 This a Sphinx based documentation. 

binder/environment.yml

@@ -1,19 +1,16 @@
+name: omero-guide-ilastik
 channels:
   - anaconda
   - conda-forge
   - ilastik-forge
 dependencies:
-  #- numba==0.48.0
-  - omero-py
+  - python==3.9.*
+  - omero-py==5.19.*
   - pip
-  - ipywidgets
-  - tornado<6
-  # ilastik
-  # see https://github.com/h5py/h5py/issues/1880
-  - h5py<3.2
-  - ilastik-dependencies-no-solvers==1.4.3
-  - ilastik-forge/label/ilastik140::ilastik-meta==1.4.0b14  # ilastik-forge
+  - ipywidgets==7.8.5
+  - ilastik-forge::ilastik==1.4.1b22
+  - ipykernel==6.29.5
   - pip:
-    - yapsy
-    - itkwidgets
-    - ome-zarr
+    - yapsy==1.12.2
+    - itkwidgets==0.32.6
+    - ome-zarr==0.9.0